BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9867837.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 25,661,723 number of mapped reads = 24,887,466 (96.98%) number of supplementary alignments = 137,656 (0.54%) number of secondary alignments = 0 number of mapped bases = 2,240,209,579 bp number of sequenced bases = 2,239,636,609 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,429,972 duplication rate = 1.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.3582 >>>>>>> ACTG content number of A's = 631,793,250 bp (28.21%) number of C's = 483,473,207 bp (21.59%) number of T's = 634,662,295 bp (28.34%) number of G's = 488,609,355 bp (21.82%) number of N's = 1,098,502 bp (0.05%) GC percentage = 43.4% >>>>>>> Mismatches and indels general error rate = 0.0046 number of mismatches = 9,741,875 number of insertions = 220,633 mapped reads with insertion percentage = 0.87% number of deletions = 226,283 mapped reads with deletion percentage = 0.88% homopolymer indels = 35.91% >>>>>>> Coverage mean coverageData = 0.7237X std coverageData = 8.656X There is a 44.64% of reference with a coverageData >= 1X There is a 15.83% of reference with a coverageData >= 2X There is a 5.03% of reference with a coverageData >= 3X There is a 1.7% of reference with a coverageData >= 4X There is a 0.69% of reference with a coverageData >= 5X There is a 0.35% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.14% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 192515602 0.7723776222808287 16.86388934671233 chr2 243199373 146701662 0.6032156258889697 4.718538057847436 chr3 198022430 149198039 0.7534400976697437 5.191938622042007 chr4 191154276 118111800 0.6178873027145885 5.8669644060793 chr5 180915260 125967136 0.6962770083629208 1.0361940360570197 chr6 171115067 135715783 0.7931258502210095 2.389680108602779 chr7 159138663 98173337 0.6169043722580477 5.682847020468475 chr8 146364022 220016091 1.503211567935732 4.566647471377148 chr9 141213431 92117374 0.6523272846475914 3.8537938588133747 chr10 135534747 133687789 0.9863728081478619 27.490015481006647 chr11 135006516 107707126 0.797792056199717 2.8210341614949033 chr12 133851895 85650221 0.6398879971030668 1.063440387034775 chr13 115169878 54018478 0.46903304004541885 0.7620546520801776 chr14 107349540 46386178 0.43210411521092684 1.086163178007326 chr15 102531392 66625640 0.6498072317207982 0.9207666442431667 chr16 90354753 84304409 0.9330379000648699 9.345253306467487 chr17 81195210 72153609 0.8886436650634932 3.0743077465198168 chr18 78077248 51889183 0.6645877554495773 7.807257012703732 chr19 59128983 42346910 0.716178561704672 10.523851276305228 chr20 63025520 52260927 0.8292026309342628 1.9637295115020164 chr21 48129895 33825125 0.7027882566542063 4.296465119556212 chr22 51304566 18620694 0.36294418707294007 0.7775089300542455 chrMT 16571 6186022 373.3040854504858 119.11555651725511 chrX 155270560 96380582 0.6207266979651519 1.8765208093028631 chrY 59373566 9649862 0.16252791688476317 8.17963755566499